Mercurial > repos > iuc > mothur_make_fastq

comparison make.fastq.xml @ 2:2a3cc9dcd6fb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:00:47 -0400
parents c49147967884
children
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1:ecbc8745f135 2:2a3cc9dcd6fb
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat && 13 ln -s '$fasta' fasta.dat &&
14 ln -s "$qfile" qfile.dat && 14 ln -s '$qfile' qfile.dat &&
15 15
16 echo 'make.fastq( 16 echo 'make.fastq(
17 fasta=fasta.dat, 17 fasta=fasta.dat,
18 qfile=qfile.dat 18 qfile=qfile.dat
19 #if $chooseformat.use == "yes": 19 #if $chooseformat.use == "yes":
20 ,format=${chooseformat.format} 20 ,format=${chooseformat.format}
21 #end if 21 #end if
22 )' 22 )'
23 | sed 's/ //g' ## mothur trips over whitespace 23 | sed 's/ //g' ## mothur trips over whitespace
24 | mothur 24 | mothur
25 | tee mothur.out.log 25 | tee mothur.out.log
26 ]]></command> 26 ]]></command>
27 <inputs> 27 <inputs>
28 <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/> 28 <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/>
29 <param name="qfile" type="data" format="qual454,qualillumina,qualsolid,qual" label="qfile - Sequence Quality file"/> 29 <param name="qfile" type="data" format="qual454,qualillumina,qualsolid,qual" label="qfile - Sequence Quality file"/>
30 <conditional name="chooseformat"> 30 <conditional name="chooseformat">
39 <option value="illumina">Illumina</option> 39 <option value="illumina">Illumina</option>
40 </param> 40 </param>
41 </when> 41 </when>
42 <when value="no"/> 42 <when value="no"/>
43 </conditional> 43 </conditional>
44 <expand macro="param-savelog"/>
44 </inputs> 45 </inputs>
45 <outputs> 46 <outputs>
46 <expand macro="logfile-output"/> 47 <expand macro="logfile-output"/>
47 <data name="fastq" format="fasta" from_work_dir="fasta*.fastq" label="${tool.name} on ${on_string}: fastq"> 48 <data name="fastq" format="fasta" from_work_dir="fasta*.fastq" label="${tool.name} on ${on_string}: fastq">
48 <change_format><!-- if set, chooseformat.format param should override qfile.ext format --> 49 <change_format><!-- if set, chooseformat.format param should override qfile.ext format -->
57 </outputs> 58 </outputs>
58 <tests> 59 <tests>
59 <test><!-- test defaults --> 60 <test><!-- test defaults -->
60 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> 61 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
61 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> 62 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
62 <output name="fastq" md5="e77b78321620e300946c23147ad599fd" ftype="fastqsanger"/> 63 <output name="fastq" ftype="fastqsanger">
64 <assert_contents>
65 <expand macro="test-fastq-format"/>
66 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
67 </assert_contents>
68 </output>
69 <param name="savelog" value="true"/>
63 <expand macro="logfile-test"/> 70 <expand macro="logfile-test"/>
64 </test> 71 </test>
65 <test><!-- test with quality score format conversion --> 72 <test><!-- test with quality score format conversion -->
66 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> 73 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
67 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> 74 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
68 <param name="use" value="yes"/> 75 <param name="use" value="yes"/>
69 <param name="format" value="illumina"/> 76 <param name="format" value="illumina"/>
70 <output name="fastq" md5="c792253da205d4d1c66bc87a2969aa25" ftype="fastqillumina"/> 77 <output name="fastq" ftype="fastqillumina">
78 <assert_contents>
79 <expand macro="test-fastq-format"/>
80 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
81 </assert_contents>
82 </output>
83 <param name="savelog" value="true"/>
71 <expand macro="logfile-test"/> 84 <expand macro="logfile-test"/>
72 </test> 85 </test>
73 </tests> 86 </tests>
74 <help> 87 <help><![CDATA[
75 <![CDATA[
76 88
77 @MOTHUR_OVERVIEW@ 89 @MOTHUR_OVERVIEW@
78 90
79 **Command Documentation** 91 **Command Documentation**
80 92
81 The fastq.info_ command reads a fasta file and quality file and creates a fastq. 93 The make.fastq_ command reads a fasta file and quality file and creates a fastq.
82 94
83 95
84 .. _fastq.info: https://www.mothur.org/wiki/Make.fastq 96 .. _make.fastq: https://www.mothur.org/wiki/Make.fastq
85 ]]> 97
86 </help> 98 ]]></help>
87 <expand macro="citations"/> 99 <expand macro="citations"/>
88 </tool> 100 </tool>